The Science of Existence – Eukaryotes


The key events in the evolution of eukaryotes were the acquisition of the nucleus, the endomembrane system, and mitochondria. ~ American evolutionary biologist David Baum & American cytologist Buzz Baum

Eukaryotes arose from an evolutionary combination of prokaryotes. The partnership proved so winning that it established an environmentally dominant domain of life.

All multicellular organisms are eukaryotes. Plants and animals are eukaryotic.

While eukaryotic cells have a more elaborate structure, basic cell functioning of prokaryotes and eukaryotes is similar.


Cellular organelles are simultaneously distinct from the rest of the cell and completely reliant on it for their identity and function. ~ American cytologists Suzanne Wolff & Andrew Dillin

A eukaryotic cell may have several thousand organelles which perform a vast variety of functions, including biochemical, regulatory, and motile processes. The composition of each organelle is tailored to its function and a cell’s immediate need.

Cells distribute and position their organelles to optimize productivity; particularly, organelle-organelle interaction. Organelles communicate with each other and work together for the cell’s benefit. Special proteins on organelles’ outer membranes recognize their counterparts on other organelles and arrange physical contact to efficiently effect sharing. Cellular processes are kept running smoothly by an intricate orchestration of molecules that flow among organelles.


Mitochondria are ancient relics of a purely single-celled world. ~ Suzanne Wolff & Andrew Dillin

Mitochondria are semi-autonomous organelles that contain their own genetic machinery. ~ American cytologist Eric Schon

The mitochondrion is a double-membraned organelle that acts as a cell’s power plant: generating a supply of ATP, the universal cellular energy molecule. Digested nutrients enter a mitochondrion and are assimilated in a way that maximizes their energy potential.

The system for optimizing the extraction of energy from food molecules is versatile, and can be modulated in unexpected ways, in order to adjust to the dietary composition of nutrients, or to the specialized function of particular cell types. ~ Spanish biochemist José Antonio Enríquez

Mitochondrial ATP production is regulated by calcium flow into a mitochondrion from another organelle. That flow is controlled by various proteins which regulate the voltage across the inner mitochondrial membrane.

From physics and chemistry standpoints, there are numerous tradeoffs that affect the efficiency of ATP production.

Nature evolved a control structure finely tuned to effectively manage these tradeoffs with flexibility to adapt to changes in supply and demand, at the cost of higher enzyme complexity. ~ Indonesian biologist Fiona Chandra et al

Besides energy supply, mitochondria are also pivotal in the cell life cycle: production of cellular building blocks (e.g., amino acids, nucleotides), cell growth, cellular differentiation, intracellular communication, and cell death. There are multiple signaling pathways between various organelles and a mitochondrion.

Each mitochondrion has compartments dedicated to specific functions. It is one of the most complex organelles.

The proteins within a mitochondrion vary by tissue and organism species. The mitochondrial proteome is dynamically regulated.

The number of mitochondria in a cell varies widely by organism and tissue type. Some cells sport only a single mitochondrion, while others may have several thousand.

Producing power for cellular needs generates heat. Operating at 50 ˚C, mitochondria run 13 ˚C hotter than the rest of the cell.

Mitochondria do their best under stress to keep working. Contents of a damaged mitochondrion may be absorbed into a healthy one, thereby salvaging still-employable machinery. New mitochondria may be created; contributing to quality control by removing damaged ones.

Mitochondrial defects can lead to a wide variety of metabolic, muscular, and neurodegenerative diseases. Mitochondria are one basis for aging, and can incite age-associated diseases, including Alzheimer’s, Parkinson’s, and heart failure.

Hence, the health of mitochondria is crucial to cell well-being, and of the entire organism. The organelle plays an essential role in mind-body interactions, with long-term health consequence.

Mitochondria contain their own genomes that, unlike nuclear genomes, are inherited only in the maternal line. ~ American cytologist Ruth Lehmann et al

Egg cells know that to get a good start in life they need reliable power plants. So, during their development (oogenesis), egg cells are choosy about the mitochondrial DNA they take with them, selecting the best available.

The mitochondrion influences an organism’s integrated response to psychological stress. ~ American pathologist Martin Picard et al

Entanglement of psychology and physiology is well documented. The importance of mitochondria to holistic health illustrates the integration of the mind-body at all scales: from organelle to organism. Such scale-independent unification suggests that organisms exist as synergistic life-energy gyres, with an emergent mind-body, in the physics sense of coming into being moment-by-moment, and with the vitality of the whole organism and constituents being reflective of each other.

With rare exception, organisms with sexual reproduction inherit only maternal mitochondrial genes. A prevailing hypothesis is that sperm mitochondria are exhausted after their fertilization competition, yielding an undesirable unreliability for genetic inheritance of this crucial capacity. Mitophagy, the process by which cells eat their own mitochondria, has a role in the selective elimination of paternal mitochondria.


Links exist between the nucleus and the extracellular microenvironment that direct cell fate. ~ American biologists Valerie Weaver & Russell Bainer

The nucleus serves as the control center of a cell, maintaining the integrity of a cell’s genes and their expression. The nucleus contains the nuclear genome, which holds most of a cell’s genetic material, though the mitochondrion and cytoplasm also hold genomes relevant to their operations.

As with a mitochondrion, a double membrane envelops the cell nucleus. Nuclear envelope proteins – nucleoporins – selectively allow molecules in and out of the nucleus. Proper functioning of these nuclear pore complexes is critical to maintaining cell health.

Amazingly, nucleoporins can manage over 1,000 molecules per second. Amino acid sequences within these proteins are optimized for efficiency in screening and transport. The physiochemical optimality of these sequences has been conserved evolutionarily from the early times of eukaryotes.

A nucleus has no membrane-bound sub-compartments but is organized for various operations. The best-known sub-nuclear body in the nucleus is the nucleolus, which is the site of ribosome assembly. A control center for cellular growth and health, the nucleolus takes up 25% of the nucleus. Malfunctioning nucleoli are a known cause of several human diseases.

Endoplasmic Reticulum

The endoplasmic reticulum (ER) is an organelle connected to the nuclear membrane; a membranous network of sac-like structures (cisternae) held together by the cytoskeleton.

The ER has a myriad of functions, including carbohydrate metabolism, lipid synthesis, glycoprotein production, and cell membrane manufacture. (A glycoprotein is a protein with an attached carbohydrate (glycan).) The ER also plays a critical role in assisting mitochondrial division and replication. The ER and mitochondria have tightly coupled dynamics via extensive contacts.

When a cell is stressed, such as suffering nutrient deprivation or oxygen shortage, proteins degrade and become damaged. The ER coordinates response, invoking a variety of techniques. Several of the repair procedures are epigenetic in nature. Others include altering DNA sequences and facilitating first-aid functions to repair the damage.

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Once inside a cell, a wide variety of pathogens hijack the ER to do their dirty work. An endangered ER signals its dilemma by releasing inflammatory proteins which set off an immune response. To avoid triggering an alarm, bacterial pathogens often inhibit ER stress response. Others employ a cagier stratagem.

Brucella abortus actively encourages inflammation in pregnant animals that it infects. Its sepsis can provoke a spontaneous abortion, releasing the infected uterine contents. Animals nearby subsequently consume the infected tissues and themselves become infected. Thus B. abortus cannily spreads.


Ribosomes translate sequences of nucleic acids into sequences of amino acids. ~ Israeli systems biologist Shlomi Reuveni et al

Although not membrane-bound, ribosomes are considered organelles. Ribosomes are protein factories; producing their products in an intricate, multi-step process. Nearly all the proteins required by cells are synthesized by ribosomes. Ribosomes receive their instructions from the cell nucleus and obtain their construction materials from the cytoplasm.

A ribosome assembles a particular protein by translating information encoded in messenger RNA (mRNA). While many ribosomes churn out a wide variety of proteins, some specialize to manufacture only certain products. A single cell may have thousands of ribosomes.

Ribosomes are composed of 55 to 80 proteins, depending on organism type. Highly ordered, these structural proteins are unusually short and uniform in length. Ribosomes also have 2–3 strands of RNA, which account for up to 70% of the total mass of the ribosome.

The ribosomes of archaea, bacteria, and eukaryotes differ in structure and composition. But the subunits within are similar between prokaryotes and eukaryotes.

The ribosome is universal biology. ~ American biochemist Loren Williams

Prokaryotic ribosomes produce proteins using a slightly different process than eukaryotic ribosomes. But the core translation mechanics of the ribosome are essentially the same in all organisms. To meet production requirements, the outer regions of ribosomes expand and become more sophisticated as organisms become more complex.

Prokaryotic ribosomes are ~20 nm in diameter and contain 65% RNA and 35% ribosomal proteins. Eukaryotic ribosomes are 25–30 nm in diameter, with an RNA-to-protein ratio close to 1. The RNA in ribosomes account for ~85% of a cell’s RNA pool. The number of ribosomes within a cell varies greatly, from less than 10,000 to up to 10 million.

Defective mRNAs result in aberrant, potentially harmful proteins; so special proteins surveil production and ensure quality control.

Ribosomal RNA itself plays a vital role in all stages of protein synthesis.

Golgi Body

Cells synthesize a sizable number of protein-based macromolecules. Some are used internally. Others are secreted for use by other cells (exocytosis).

The Golgi body is a stack of membranes that works in concert with an ER to package proteins before shipping the proteins off to their intended destination. Enzymes tune up newly synthesized proteins in the Golgi to improve their job performance potential.

In animal cells, the Golgi mysteriously breaks up and disappears at the onset of cell division (mitosis), reappearing during the telophase of mitosis: when 2 daughter nuclei form in the cell. In contrast, Golgi stacks stay intact through the cell cycle in yeast and plant cells.

Plasma Membrane

The ability of organisms to form fluid structures of some rigidity in an aqueous environment is central to the existence of life on this planet. ~ American physicist Peter Collings

The contents of every cell are held within a plasma membrane, which is a flexible container of controlled permeability. The cell membrane supports its cell and helps maintain its shape. Cell membranes are living liquid crystals: able to maintain a necessary, delicate balance between fluidity and rigidity. The structure of the plasma membrane is similar in prokaryotic and eukaryotic cells.

Organelles within cells are also enclosed within a membrane. As an evolutionary artifact of endosymbiotic incorporation, the nucleus, mitochondria, and chloroplasts in plants have 2 membranes.

Cell membranes are a mix of proteins and lipids, with respective percentages varying by cell type. While lipids structure the cell membrane, proteins manage traffic through the membrane and keep the membrane in good working order. Cell membranes are organized into distinct domains, with different proteins performing a range of necessary functions.

The lipid composition of membranes can have profound effects on the behavior and activity of its resident macromolecules. ~ Eric Schon

3 lipids are employed in cell membranes: phospholipids, glycolipids, and sterols. While the amount of each varies by cell type, phospholipids are consistently the most abundant.

The cell membrane scaffold is a double layer of phospholipids. A phospholipid has a hydrophilic (water-loving) phosphate head and 2 hydrophobic (water-fearing) fatty-acid tails. Phospholipids spontaneously arrange themselves into a double-layered structure, with their hydrophobic tails pointing inward and their hydrophilic heads facing outward. Most biological membranes have this energetically favorable 2-layer structure, called a phospholipid bilayer.

A glycolipid is a lipid with sugar on top. In cell membranes, glycolipids self-assemble into highly organized domains. Glycolipids situated on a cell membrane surface act as signal markers, facilitating recognition by other cells. Their specific arrangement regulates numerous cellular processes which can cause disease if not properly done.

Lipids are hydrophobic. Their natural aversion to water causes them to clump together. That only partly explains the intricate integration of glycolipids on a cell membrane.

The sugar molecules in neighboring glycolipids interact to form an ordered crystalline structure, connected by hydrogen bonds. Thus, both lipid and carbohydrate molecules complement each other in forming well-organized glycolipid clusters.

All sterols share a common property: the ability to regulate dynamics in order to maintain membranes in a microfluid state where they can convey important biological processes. ~ French biochemist Erick Dufourc

Sterols are essential in eukaryotic cells. In animal cells, cholesterol disperses between membrane phospholipids, keeping cell membranes from becoming too stiff, by preventing phospholipids from being too tightly packed together. Plant cell membranes lack cholesterol, opting instead for a sophisticated mix.

In contrast to animal and fungal cells, which contain only one major sterol, plant cells synthesize a complex array of sterol mixtures. Sterols regulate membrane fluidity and permeability in a similar manner to cholesterol in mammalian cell membranes. Plant sterols can also modulate the activity of membrane-bound enzymes. ~ French molecular biologist Marie-Andrée Hartmann

A cell membrane protects the integrity of the cell, policing the molecules that go in or out. From without and within the cell, a cell membrane must process a wide variety of signals to initiate apposite responses to changing conditions.

Membrane dynamics is essential for cellular life. ~ Erick Dufourc

Membranes are constantly changing, allowing migration of proteins and other products. This fluidity is essential for engulfing food, discharging waste, and secreting cellular products.

Membrane proteins act as border guards, membrane maintainers, cellular communicators (signalers and receivers), nutrient jitneys, and enzymatic actors playing various roles. Generally, there are 2 types of proteins associated with a membrane. Integral membrane proteins are inserted into a membrane and may pass through the membrane. Portions of these transmember proteins may be exposed on both sides of the membrane. Peripheral membrane proteins are on the exterior and connected to the membrane via interactions with other proteins.

Every cell is mostly water. Maintaining cell pressure, an essential function, means managing the flow of water.

Animal cells move about by managing water flow. Cell motility requires tightly regulated membrane dynamics and snappy cell shape change in the cytoskeleton. A moving cell is a symphonic exercise, conducted by certain proteins. Morphogens are signaling molecules that tell a cell where to go.

Aquaporins are proteins that act as channels for the flow of water across biological membranes in response to osmotic pressure changes. They provide the plumbing system for cells. Each aquaporin acts as a meticulous membrane pore.

All sorts of molecules pass through cell membranes, albeit selectively. Aquaporins permit the flow of small polar molecules, such as glycerol, while blocking others. As keeping electrical homeostasis is crucial, protons and certain ions are precluded passage.


Within the membrane, a gel-like cytoplasm holds a cell’s internals. The viscous liquid – cytosol – distributes needed substances throughout the cell. Proteins within cytosol intelligently manage the necessary processes.

Cytosol is 80% water. It is usually clear.

Most cellular activities happen within the cytoplasm. The flow of calcium ions in and out of the cytoplasm is how metabolic processes are signaled.

Calcium is a key to regulate many fundamental processes in cells. ~ Indian biochemist Muniswamy Madesh

Owing to its easy reactivity, calcium is a key bioelement. Calcium charges are essential to powering mitochondrial processing. Heartbeats happen as heart cells synchronously work calcium channels. The physiological correlate to thought processes within the glial cells of the human brain transpire via waves of calcium ions.


Nestled amidst the cytoplasm is the cytoskeleton: tubular filaments of protein termed microtubules, which provide cellular scaffolding and form the internal structure of cell tails – both cilia and flagella. Cytoskeletal elements extensively and intimately interact with the cell membrane.

Tubulins are the family of proteins that comprise microtubules. Tubulins are the guides by which cells know their internal organization. The asymmetric configuration of cells, whether prokaryote or eukaryote, and even left-right organ placement in multicellular organisms, owes to tubulins driving patterning during development. How tubulins know and coherently provide their orientation guidance is a mystery.


The cellular patterns by which tissues and organs develop in a multicellular organism owe to the energetic database which materializes as genetics. But cell fate is also influenced by nutritional history.

What a cell takes in during its early development is a determinant in what it will become. Hence biases in development patterns of cell fates emerge from environmental signals.

Cell Wall

A tough but flexible cell wall surrounds the membrane, giving a cell structural (tensile) strength and protection from physical damage and attack by pathogens. Although it acts as a filter, a cell wall is also permeable.

A cell wall most importantly acts as a pressure vessel, preventing over-expansion when water flows into the cell. Cytolysis (osmotic lysis) happens from an osmotic imbalance, namely excess water getting inside a cell, causing the cell to burst.

Archaea and bacteria have cell walls. Bacterial cell walls are made of peptidoglycan: a polymer comprising sugars and amino acids, forming a mesh-like layer outside the plasma membrane. Archaea have various cell wall constructions.

Plants and fungi have somewhat similar cell walls, made of cellulose and chitin. As the concentration of solutes outside plant cells is typically less than inside, cell walls are critical in maintaining structural integrity.

Protozoa and animal cells, with rare exception, lack cell walls. Animals have connective tissues – bone and cartilage – to provide structural reinforcement. Animals regulate osmotic pressure by excreting excess water and salts, and by pumping ions across cell membranes.

Further, cell walls could be a handicap to animals by restricting movement. Muscle cells could not contract if they were encased in cell walls. Hence cell walls in animals are superfluous.


Once considered merely a vestige of evolution, cilia are in fact essential to many of the body’s organs. ~ American medical science writer Mary Beth Gardiner

While a wall or membrane separates every cell from the outside, knowing what’s outside is critical to knowing what to do, or one’s role in the larger organismic scheme of things. And being able to get around may be just as essential.

Thus, almost all cells – whether prokaryote or eukaryote – have tails. Eukaryotes evolved from a tail-bearing prokaryote. Only seed-producing plants have cells without tails, though their genomes retain the knowledge of how to make tails.

Cell tails serve 2 purposes: motility and perception.

Tails may be a single whip-like flagellum or solitary sensory cilium, or a multitude of short hair-like cilia on the cell lining.

Mammalian sperm cells have a flagellum, which propels them toward a fertile destiny with an egg. Female eggs have rows of cilia, by which they make their way from the ovaries to the uterus.

Regardless of type, appearance, and motion, cell tails are structurally similar, and their employment selfsame. Each tail has fibers – microtubules – which rapidly shift positions among each other via a proton flux, generating movement. This set of fibers is enclosed in the membrane.

The electrochemical proton flux that propels tails is coordinated through membrane pores. Flux flow determines a tail’s speed limit.


Spirochetes are spiral-shaped, free-living, anaerobic bacteria. They are prokaryotes on the prowl. Having no need of oxygen indicates an ancient lineage.

Spirochetes are found in a wide variety of habitats, from swimming in mud to the guts of desert termites.

As a disease organism, a spirochetal bacterium, Treponema pallidum, causes syphilis in humans.

Spirochetes swim via a curious corkscrew motion, like the swiggles of sperm cells heading to an egg.

Some free-living spirochetes attach themselves to larger cells, providing propulsion. A taxi-driving spirochete gets its fare from leftovers of its cellular passenger.

Spirochete cilia are a ring of microtubules, like spun wires in an electrical cable. Some spirochete sport fine filaments spun from the same protein from which eukaryotes form microtubules. A characteristic animal pattern is 9 double tubules in a ring, with another double tubule holding down the middle, in a hub-and-spoke configuration.


Other bacteria prosper with different propulsion: flagella with helical filaments, driven by a rotary engine anchored on the inner cell membrane.

Flagella and cilia both work in coordinated fashion, albeit differently. Cilia move with a complex 3-dimensional swim, propelling with a power and recovery stroke.

Flagella rotate like a propeller rather than beating back and forth. These flagella are helical, and revolve 200–1,000 times per minute, propelling bacteria as fast as 60 cell-lengths per second. A cheetah, the fastest land animal, has a top speed of 25 body lengths per second.

Though similar structurally, the proteins that make up cell tails differs between bacteria, archaea, and eukaryotes. This suggests that tails are an instance of convergent evolution: coming to the same solution independently.


Paramecia have 2 sets of selfsame cilia. One puts a move on, while the other facilitates feeding, by sweeping nutrients into oral grooves.

Paramecia locomotion cilia are powered by a different motor than feeder cilia. Viscosity slows paramecia motion, but feeding cilia are unaffected. Getting around is less important than chowing down.


Tails are crucial cellular sensors. Depending upon type, cell cilia can sense fluid movement, chemicals, osmotic pressure, temperature, and/or gravity.

Mammalian adaptive immune system T-cells have no apparent cilium, but they do have the equivalent. The synapse that activates a T-cell acts like a cilium and is built much the same.

Cilia are critical to intercellular communication. In animals, they help maintain organ function via continuous feedback loops. In epithelial tissues, the cilia of host cells may actively recruit microbial symbionts.

The asymmetry of human bodies is established within a few hours after an embryo begins developing. This is done by the tails of cells sweeping clockwise, generating a net leftward flow, which tells left from right, and determines situs solitus: the position of organs.

Damaged tails often spell cell death. If the cilia of cells cannot function, disorders arise. Badly behaved or non-functioning cell tails are instrumental in many diseases.


The creative endeavors of ribosomes have clean-up counterparts. Worn-out organelles, waste materials, and cell debris must be swept up and recycled or disposed. This process is termed mitophagy. In contrast, autophagy is the process of removing a cell too worn-out to carry on anymore.

Mitophagy plays a critical role in cellular health. In humans, its disruption contributes to systemic degeneration, including intelligence system and cardiac diseases, diabetes, and cancer.

Lysosomes are a cell’s waste disposal system. Plants have lytic vacuoles that serve the same function. These organelles contain acid hydrolase enzymes which break down cellular debris. Lysosomes digest the macromolecules from phagocytosis, endocytosis, and mitophagy: processes which ingest matter that needs recycling. Lysosomes also transport undigested material to the cell membrane for expulsion.

Cell organelles constantly monitor themselves. When an organelle no longer functions as it should, pro-mitophagy agents have the organelle mark itself on its membrane for delivery to the cell’s recycler (lysosome or lytic vacuole). The same chemical marking is used for both organelle mitophagy and cellular autophagy.


Aging seems to be the only way to live a long life. ~ French composer Daniel Auber

Programmed cell death (apoptosis) is part of life. During development, certain cells must surrender their lives to advance an organism to the next stage. Fingers emerge from paddle-shaped hands by apoptosis of the cells that form the webbing between digits-to-be.

Dying cells interact with their neighbors. They can send signals for other cells to proliferate and tell cells from afar that it is time for them to die too.

Good health depends on the strict regulation of cell division and cell death. Apoptosis — a kind of suicide plan for cells — is an important safety mechanism for the body to get rid of damaged, aged, or unneeded cells. ~ German cytologist Stephanie Bleicken

Cell death can run amok: killing cells in excess after a traumatic event, such as a heart attack or stroke, or in the course of degenerative diseases, such as Alzheimer’s. Normally cell death is meticulously decided and controlled.

The apoptotic control network includes several positive feedback loops. Apoptosis spreads through trigger waves. ~ American systems biologist James Ferrell Jr. & Chinese cytologist Xianrui Cheng

Cell death begins with biochemical trigger waves. Once initiated, specific killer proteins in the cell, called caspases, activate.

When a cell is dying, it goes through a characteristic series of morphological alterations and, in the end, it is engulfed and digested by neighboring cells. ~ German cytologist Barbara Conradt

A cell undergoes a series of changes – altered protein production and gene expression – as it dies. Even during demise cells struggle to survive with remarkable resilience: able to bounce back from poisoning if the toxin is removed (anastasis, Greek for “rising to life”). The point of no return, when cell death is irreversible, is not yet known.

The Evolution of Eukaryotes

Everything you’ll ever need to know is within you; the secrets of the universe are imprinted on the cells of your body. ~ American author Dan Millman

As the Earth and its atmosphere were transformed by cyanobacteria, viruses promoted prokaryotic evolution by providing genetic uploads.

~2.5 BYA, eukaryotes arose. The first step to eukaryotic life was through unification: one prokaryote incorporated another. The host was an archaeon.

An intracellular bacterial parasite gave rise to the mitochondria found in all eukaryotic cells. At some point, the bacterium that beget mitochondria became benign, then mutualistic. The mitochondrial bacterium went from stealing ATP to providing it.

Transition to accommodation is not unusual. Viruses go from devastating to their hosts to being tolerable or even beneficial, as they learn to prolong their residency by not inflicting untold damage, and thereby benefit from host longevity.

Mitochondrial incorporation came late in the evolution of eukaryotes. Already many eukaryotic hallmarks, including complex subcellular organization, were in place prior to added a dedicated power plant facility to the works.

 Colonial Choanoflagellates

Bacteria are the important part of the multicellular story. ~ American cytologist Nicole King

Choanoflagellates are free-living unicellular and colonial flagellate eukaryotes. These plankton are the closest living relatives of animals.

In a colony, choanoflagellates are more than an aggregation. Instead, they are an interacting cluster, demonstrating the basic mechanics for multicellularity.

Colonial choanoflagellates only exhibit this behavior under the influence of resident bacteria. Bereft of bacteria, they do not inch toward acting in a multicellular manner.


Evolution is adaptation guided by energy economy. Hence the evolution of eukaryotes was a matter of task division according to relative performance of the different cells involved. A common genetic foundation afforded the necessary chemical communication network. This furthered adaptation geared to efficiency: the least energy expended to produce the desired result.

Over evolutionary time, most of the genes housed in the former bacterial endosymbiont, now mitochondrion-bound, migrated to the genome of the archaeal host. These genes became enclosed in a protective membrane, forming the cell nucleus.

The genes that stayed in the mitochondria were those needed for practicing its core business: coding for proteins which maintain redox balance, which must be synthesized locally to counteract the otherwise deadly effects of ATP-generating electron transport.

In modern eukaryotic cells, the mitochondrial genes resemble those of bacteria, while the original nuclear genome resembles a heritage of bacterial and archaeal origin. Eukaryotic DNA replication descends from archaea, not bacteria.

The acquisition of the mitochondrial power plant gifted eukaryotic cells with 200,000 times the energy available to the average prokaryotic cell. This enabled eukaryotic cells to expand their volume by up to 15,000 times that of the typical bacterium, and to support a genome 5,000 times larger.

After the 1st union of prokaryotes, one or more proto-eukaryote cell types had a 2nd round of endosymbiotic uptake.

Photosynthesis was acquired by endosymbiosis. The ancestor of light-fed algae and progenitor of plants incorporated a cyanobacterium, thus picking up chloroplasts. A chloroplast is the photosynthetic organelle found in algae and plant cells. It is a type of plastid.

Plastids is the catchall term for the major organelles found in the cells of plants and algae. Various plastids have different functions, such as storing starch or fat, or detecting gravity. Some plastids have several internal membrane layers, indicating an independent heritage of endosymbiont incorporation. Algae plastids typically differ from plant plastids.

Like the previous incorporation leading to proto-eukaryotes, many genes of the consumed cyanobacterium that became a chloroplast migrated to the host cell genome. Mechanisms evolved that allowed the proteins encoded by transferred genes to work for the chloroplast colonizer, so as to photosynthesize.

The plastid genome that remained kept its legacy of cyanobacterial origin. But the nuclear genome of plastid-containing eukaryotes is chimeric: containing both the proto-eukaryotic genome and genes derived from the cyanobacterial genome.

The genes to make the enzyme that manufactures the amino acid phenylalanine (Phe) was lifted from an ancient bacterium. Phe is used in many plant products, including lignin, which is critical for the strength of plant cell walls. For animals, Phe is an essential amino acid.

The incorporating evolution of eukaryotes was a milestone, but not as novel as once thought. Some bacteria have protein shell subunits which are functionally equivalent to eukaryotic organelles. Efficiency by division of labor, along with cooperative communication and coordination, existed even in early prokaryotes. There are numerous known examples of cooperative exchange and intimate relationships among prokaryotic microbes.

However impressive in effect, it is only an incremental step from prokaryotic cells aggregating, and sharing genetic material (plasmids), to cooperative envelopment involving different lineages of prokaryotes. Hence, multicellular life was an incremental adaptation from single-celled organisms. In aggregate forms, prokaryotic cells communicate, communally make decisions, and even differentiate; quite like organelles within eukaryotic cells, which communicate and coordinate; as do cells themselves within multicellular organisms.

Larger eukaryotic cells offer efficiencies as well as room for more sophistication. And so more complex organisms are eukaryotic. But there are tradeoffs.

Compared to eukaryotes, smaller size gives prokaryotes a greater surface-area-to-volume ratio, which translates to a higher metabolic rate and a faster growth rate, resulting in shorter generation times. This speed advantage, coupled with horizontal gene transfer, yields a formula for the rapid adaptive capabilities that microbes are known for. Horizontal gene transfer is the environmental depositing and pickup of genic packages which contain actionable intelligence. Bacteria are in the business of being genetic quick-change artists; as are viruses, which carry even less baggage than prokaryotes.


The presence of mitochondria and related organelles in every studied eukaryote supports the view that mitochondria are essential cellular components. This organism has evolved beyond the known limits that biologists circumscribed. ~ Polish molecular evolutionary biologist Anna Karnkowska

Metamonada is a large group of anaerobic flagellate protozoa. Most live as symbionts in the guts of animals, from insects to mammals. Protozoa are a diverse phylum of unicellular eukaryotes, partly classified together for their various abilities to live in harsh environments.

Metamonads get by without mitochondria, thanks to a cytosolic mobilization system that they acquired from bacteria. This system substitutes for essential mitochondrial functions.

In being an apparent step back toward prokaryotes, the loss of mitochondria is an instance of reversion evolution. Despite having no mitochondria, metamonads have otherwise sophisticated eukaryotic cells.

Eukaryotic Uplift

Geology played a part in eukaryotic evolution, notably in copious delivery of useful compounds.

Earth’s landmasses collided and created the supercontinent Nuna 1.9 BYA. As Nuna was nudged into being, molten mantle material made its way to the crust and crystallized, forming a rare type of granite that began eroding quickly, distributing quantities of metal sulfides to coastal areas. This introduction enhanced the biogeochemical environment; a welcome gift to evolving biota. An ampler supply of zinc – a trace element employed by microbes, plants, and animals – was one such delivery.

Its geological enrichment accomplished, Nuna began to fragment 1.5 BYA.

Eukaryotic Cell Types

Diversification of cell types afforded the evolution of multicellular organisms. The simplest are made of a few dozen different cells, while humans are composed of over 200 kinds of cells.

Somatic cells are the ordinary cells of a multicellular eukaryote. These cells are the basis of the 4 primary animal tissue types: epithelium, muscle, connective, and intelligence tissues.

Epithelial tissues line the surfaces and cavities of bodily structures and form many glands. These cells secrete, selectively absorb, protect, and transport.

Muscle cells, being capable of contraction, provide for movement. Muscle is the most abundant tissue in most animals.

Connective tissue supports, separates, or connects other tissues. Connective tissue, immersed in body fluids, is composed of cells, fibers, and extracellular matrices.

In some animals, including vertebrates, the body physically centers its intelligence system in glial cells, which are networked together via neurons. 85% of human brain cells are glia. (Whether cell or organism, an intelligence system is energetically driven by a mind.) Glia nurture and control neural growth and activity within the brain, as well as receiving neutrally transmitted information from external stimuli for further processing.

Stem cells, found in all multicellular life, are cells of flexible form, able to differentiate into diverse specialized cell types, including somatic cells. Stem cells guide organism development. Stem cells can also self-renew: stir up more stem cells.

There is a fitness advantage to renewing your mitochondria. Stem cells know this and have figured out a way to discard their older components. ~ American biologist David Sabatini

Stem cells intelligently manage their resources: providing the highest-quality organelles to daughter stem cells. Such strategic thinking lessens cellular damage that can lead to stem cell exhaustion, thereby aging an organism from reduced tissue renewal.

By dividing asymmetrically, stem cells can generate two daughter cells with distinct fates. Stem cells segregate their old mitochondria to the daughter cell that will differentiate, whereas a new stem cell will receive only young mitochondria. ~ Finnish cytologist Pekka Katajisto

If there is a shortage of stem cells, differentiated cells can take their place: generating various cell types, including more stem cells. Genes dormant in differentiated cells again become active when reverting back to stem cell status.

Germline cells are the special cells of sexual reproduction, producing gametes. In animals, the gametes are eggs and sperm. Plant germ cells produce ovules and pollen.

Animal germ cells develop in the embryotic stage. In flowering plants, germ cells come from somatic cells in adult floral meristem: the plant tissue where growth occurs.